The Wrong Choice
by temporaryhome
Summary: They went to Neverland to find Henry and succeeded. When they come back, Neal is waiting for Emma down by the docks. Emma thinks getting back together with Neal is the best thing for Henry, but what about her Captain? R&R, pretty please. Short story
1. Chapter 1

**I don't own any of the characters. **

**I really hope you like it. Don't forget to review, pretty please. **

**Story line:** They went to Neverland to find Henry and succeeded. When they come back Neal is waiting for Emma down by the docks. Emma thinks getting back together with Neal is the best thing for Henry, but what about her Captain?

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They had all been back from Neverland a couple of weeks now and there were still celebrations going on in their little town. It had taken them months to find Henry and when they finally found him, they had to battle their way out again. Emma was glad everyone had gotten back safely and she also knew who made sure they all did, Killian Jones or otherwise known as Captain Hook. She hadn't seen him since they had arrived back in Storybrooke. They had gotten pretty close while being on their journey, even almost kissed a few times as well, but it all had changed when they had found Henry. She was overjoyed that he was back and didn't have eyes for anyone else but him. It even got worse when they arrived back in Storybrooke and Neal was waiting for them.

_-Flashback-_

_They couldn't believe they had made it back from Neverland. Emma held Henry tight and smiled. Everyone was waiting for them by the docks, happy and cheering that they had finally arrived back after seven months. Emma swiftly looked at Killian and saw he was looking right back at her. Staring into her eyes with those bright blue eyes. Emma smiled at him as he winked at her. Killian had been there for her even when she didn't realize she needed someone. She always had her brave face on, her poker face, but Killian seemed to see right through it. It truly annoyed her in the beginning, but she secretly liked it too. She could count people like him on one hand. He had promised they'd find her son and she trusted him. He had almost lost his own life a couple of times in order to save Henry. She had come to see him in a new light._

_As they descended from the Jolly Roger, she saw Neal coming up towards them, hugging them both like there was no tomorrow._

"_Dad? You're alive!" Henry said. Neal nodded and kissed his forehead and before Emma realized what was happening he kissed her on the lips. She pulled away slowly not wanting to hurt Neal's feelings. She looked back for Killian, but he had already retreated to his quarters._

_-End of flashback-_

After that Neal and her had slowly gone back to being a sort of couple again. Emma still loved Neal, but she wasn't in love with him anymore. Neal broke her, left her and hurt her to no end, but for Henry she would do anything. She wanted him to have a normal life, normal parents – as normal as one can be being the grandson of Snow White, Prince Charming and Rumple. She wouldn't let Neal sleep over nor touch her in anyway. It just didn't feel right when he tried to come closer to her.

"Hey babe," Neal said and kissed her. Emma stiffened a little, but Neal didn't notice. He never noticed anything though. She still had to talk to him about keeping the relationship platonic, but she was afraid he would leave and hurt Henry in the process.

"Hey kid," Emma said smiling at Henry came up to her for a hug. "How was school?"

"Fine, mom," Henry said and smiled. "Same old, same old."

Emma had tried to cook dinner, but failed miserably so they decided to go to Granny's Diner. As they passed the docks, Emma let out a small sigh. She should really visit Killian; she never even had thanked him for what he did.

'You okay, mom?" Henry asked and he looked at her knowingly. "Sure, kiddo. Just glad it's all over now,' she said and smiled, but he couldn't fool him.

When they arrived at the diner, Henry was telling a joke Charming had told him earlier making her and Neal laugh. She stiffened a bit when she saw Killian sitting in one of the booths with no one other than her mom, Snow White. He looked at Emma, dark circles around his eyes and his eyes not so bright anymore. He had traded his pirate attire for normal clothes: faded jeans and a blue button-down shirt. It looked great on him. She smiled at him, but got nothing in return. His eyes went to Neal's arm that was resting on her waist without her even knowing it was there.

"Hey guys," Emma heard Mary Margaret say.

"Grams," Henry said smiling and hugged her and then turned to Killian to hug him too. "Hey Captain Killian."

Emma instantly felt warm at the sight in front of her and couldn't stop the small smile from showing on her lips.

"You want to have dinner with us?" Henry asked both of them, making Emma tense. "Henry," Emma started, but Killian interrupted her.

"No need, Swan," he almost snapped at her, before looking at Henry and smiled. 'Thanks for the invite, lad, but I was on my way out anyway."

He stood up saying thanks to Mary Margaret and left the diner. Emma felt a strange thug in her chest, a small painful thug, watching him leave.

She wanted to talk to him so badly. She excused herself and ran after him before she even realized what she was doing.

"Killian!" she shouted, making him turn around. He looked surprised for a second, but quickly changed his expression to blank.

"Can we talk?" Emma asked not daring to look into his eyes. She heard him sigh quietly. "What about, Swan?"

Emma felt as if someone had just punched her when he called her Swan. No Emma, no lass, no love, just Swan.

"I've never gotten the chance to say thank you for everything you did," she said looking up to him. He smiled grimly at her and nodded.

"You are welcome," he said and started walking away.

"Wait-" Emma said and grabbed his left arm feeling a spark when she touched him. "I need to explain why I went back to Neal-"

"Don't," Killian interrupted her and shook his head. "I understand, you don't need to explain yourself. I just want you to be happy even if it's not with me."

"Killi-" Emma tried again, but he just shook his head and walked away from her. She sighed as she watched him go, contemplating whether or not to go after him. She decided not to complicate things and just let him be, but couldn't help but feeling weird thug in her chest again.

She walked back to the diner and saw Neal and Mary Margaret discussing something. As she came closer, she realized it was about Killian. They stopped talking for a second as they saw Emma approaching them.

"Why did you go after him?" Neal said, stressing the word him as if he was talking about garbage. Emma felt angry with Neal for talking about Killian like that.

Emma had no idea what to answer. She looked at Mary Margaret who smiled knowingly, "I just wanted to talk to him," she answered and shrugged.

"What about," Neal asked and frowned.

"I'm sure that's none of your business, Neal," Mary Margaret answered. Neal glared at Mary Margaret for a second before looking at Emma telling her they would continue this conversation later.

"Does Charming know you were here with _him_," Neal said, focusing on Mary Margaret now.

"What are you insinuating, Neal," Mary Margaret said and glared at him.

"Well, I was just saying-," Neal started, but Mary Margaret interrupted him. "Of course, David knows I'm here and that I was talking to Killian."

Emma's curiosity grew larger every minute.

"What were you guys talking about?" Emma asked quietly, glancing back at the door wishing Killian would come back in.

"I was just thanking him for saving our life … a couple of times," Mary Margaret said and smiled. Her mother was keeping something from them, but Emma decided not to pressure and ask her later on. "I need to go too. Promised David I would keep him company during his shift at the station," Mary Margaret said and hugged Henry again before hugging Emma. She gave Neal a small smile and left as well.

To say Emma was confused was an understatement. The three of them ate dinner in silence as Emma went over their conversation again. She couldn't stop thinking about how Killian had looked. She was worried about him. She wanted to go and try to talk to him again, but she was afraid that he would see right though her poker face again. Neal kept glancing at her and tried to start a conversation, but she just didn't feel like it.

"Mom, do you think Killian would want to teach me how to sail?" Henry suddenly asked, making Emma drop her fork.

"I-," she started, not knowing what to say. "I don't know, Henry. Maybe you should ask him next time you see him."

Henry nodded and smiled, all excited to ask Killian. Emma glanced up at Neal and saw him glaring at her. "What?" she mouthed at him.

"I don't want Hook near my son," he quietly said, making sure Henry didn't hear. Emma wanted to punch him right there.

"He's my son too and Killian saved our ass, especially Henry's, so don't you dare."

"Did something happen between you and him?" Neal asked frowning.

Emma glared at him and sighed.

"You ready to go, kid?" Emma asked Henry. "You need to be at Regina's in half an hour."

"Sure," he said and nodded. Emma asked for the bill. After paying it, they all got up and left. Emma was feeling really pissed off at Neal because of what he said about Killian. She just couldn't help but wanting to yell at him. She had no idea where this was all coming from. Yes, she liked Killian, more than she should, but it was crazy how she reacted when people talked about him.

They dropped off Henry and went back to the apartment.

"You didn't answer my question," Neal stated.

"What?" Emma asked.

"About Hook, did you two hooked up?" Neal said and laughed at his own joke. Emma rolled her eyes. "No," she said.

Neal laughed at that and she could see he didn't believe her, even when she was telling the truth.

"Is this why you don't let me touch you? Or let me sleep over?"

"No, I don't want you to touch me because you broke me and left. Then when I found you, you were getting married to Tamara even though you knew I was in Storybrooke. You didn't even come here; we had to go look for you. The only reason you are in the same room with me now is Henry," Emma replied, feeling relieved she had finally said this.

"I-," Neal started, but Emma interrupted him. "Save it, Neal. Please just leave."

She was so sick and tired of pretending she was in love with Neal. However, it seemed like she wasn't doing a great job anyway, remembering her conversation with her mother a couple of days ago.

_-Flashback-_

"_You don't look happy, Emma," Snow said and sighed. "You don't need to do this to yourself."_

"_I don't care about being happy, I just want Henry to be happy," Emma said. "He had to grow up without me and Neal. I just want to give him the family experience."_

"_You know that Henry doesn't care for that. He only wants you to be happy," Snow said and shook her head._

_-End of flashback-_

She went to sit on the couch and sighed. She had totally messed things up. Neal was an asshole, Killian hated her and Henry would hate her too if he would know the things she said to Neal. She felt tears coming to her eyes as she replayed the way Killian had acted. He had looked tired and sad, but also really distant. A tear rolled down Emma's cheek and soon more followed.

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**Next chapter coming up soon. Review and I will love you forever.**


	2. Chapter 2

**Disclaimer: None of it is mine. **

**Thank you so much for your lovely reviews! They made my day over and over again. **

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She woke up the next morning and realized she was still on the couch. She was getting ready for work as she heard a soft knock on her door. Her stomach dropped as she thought Neal had come back, but let out a breath of relieve when she saw David instead.

"Hey kid," he said and smiled at her.

"Hey Dav-Dad," she replied and smiled. "What are you doing here?"

"I just wanted to check if you were alright. Snow told me what happened last night," he said, looking worried.

"I'm fine," she answered. "Neal was just being a jerk as always."

David laughed at that. "I have to agree with you there. There's something else I needed to talk to you about," he said, sounding hesitant as if he wasn't sure if he should mention it. Emma started getting nervous by how he was acting and she could feel it was going to be bad news.

"Well, -," he started, but got interrupted by Neal approaching the apartment.

"Neal," David nodded stiffly and looked at Emma. "I'll talk to you later."

"No, wait! What did you want to tell me," Emma said. She needed to know.

David looked at Neal, "Give me a moment with my daughter."

Neal nodded reluctantly and moved away from them.

"He's leaving, Emma," David said and Emma knew exactly who he was talking about. Her stomach dropped and she felt as if they had just punched the life out of her. Her mind went in overdrive and her heart was pounding. She shook her head, trying to keep the tears at bay.

"Why?" she whispered.

"You know why, Emma," David said and smiled sadly. "I have to go now. I'm getting too old for the nightshift." He was trying to make her smile, but her thoughts were somewhere else entirely. She mumbled, "Thanks Dad." And he knew what she was talking about. He kissed the top of her hair and said he would take her shift at the station, so she could think about all of this. She couldn't stop the tears from falling this time and mumbled a thank you again before he turned to leave.

Neal came back towards her as David left, but she really didn't feel like talking to him.

"Not now, Neal," she snapped and shut the door with a slam.

She started hyperventilating. He couldn't leave, could he? After everything, he couldn't just leave her. But she knew he was leaving because of her, to make life easier on both of them. She had to talk to him; she had to make him stay, but could she give him what he wanted? What they both wanted? She had Henry to consider and she did want him to have a normal family.

She dropped herself on the couch again with a million things going through her mind.

She was still deeply lost in her thoughts and didn't hear Henry come in at all.

"Mom, can I ask you something?" Henry asked, making her jump in surprise.

"I didn't hear you come in," Emma said, putting her hand over her chest. She looked at the clock and was surprised it was already this late.

"Sorry, Mom," he said and smiled. "So about that question?"

"Of course, kid," she said and laughed silently.

"Why are you and dad together?" he asked. Emma looked at him and tilted her head aside.

"Because we want you to have a normal family," she answered truthfully. The kid had her ability to read people so she couldn't bear to lie to him.

He shook his head and sighed, "Mom, I'm the grandson of Snow White, Prince Charming and Rumple, I can never have a normal family." Which made Emma laugh, he was right, "and honestly, I love it."

"I know you don't love Dad. I know you love someone else and I'm totally fine with it," he continued. He was way too smart for his age.

"I'm not in love with anyone, kiddo," Emma replied with a soft smile.

"I'm not dumb, Mom. I can see the way you and Killian look at each other. And I see the way you stiffen when dad comes too close to you," he said and laughed at his mother's expression. Her face had turned pale, mouth open, eyes ready to pop out.

"I-," she started, but for once she had no idea what to say. Was she in love with Killian? Honestly, she didn't know. Sure, he was handsome, nice, there for her when she needed it, and even his innuendos weren't so bad after all. She liked having him around her, he always knew the right thing to do or say.

"You okay, Mom?" Henry asked and laughed again. "Looks like you're doing some heavy math in your head."

She looked at him with a smile and shook her head. "I was just trying to comprehend what you were saying right there."

"About you and Killian? Mom, everyone knows it," he said laughing.

"What are you talking about?" Emma replied utterly confused.

"Everyone can see the way you look at each other, even Dad. Why do you think he's always trying to steer you and me away from the docks."

"Kiddo, I really don't know what you're talking about and it's time for homework," Emma said, not wanting to think about this anymore.

Henry rolled his eyes –yeah, totally her son-, but stood up without a complaint and went to his room to work on his homework.

Emma still wasn't sure about what had just happened. Did her son give her permission to date Killian? The thought made her laugh out loud. Surprisingly, the thought of dating the fearsome pirate didn't scare her at all. In fact it made her heart flutter a bit. In that moment, she knew what she had to do. She called Mary Margaret asking her to watch Henry for a bit because there was something she needed to do before it was too late. She prayed with all her heart she wasn't already.

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**I know it's been done before, SORRY! I just wanted to make my own story with this plot. Next chapter coming on Wednesday, it'll probably be the last chapter.**

**Please review, they make me smile like crazy.**


	3. Chapter 3

**Thanks again for the reviews. You don't know how much they mean to me. **

**Disclaimer: as before none of it is mine.**

**I was supposed to update yesterday, but something came up. I'm so sorry!**

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The darkness of the night slowly faded into morning. Killian stood at the helm, watching the sun rise, the beams reflecting in the ocean. This was it. He had stolen some magic beans from the giant and was ready to set sail into the unknown. He wasn't sure which way he was heading yet, as long as it was far away from Storybrooke, from _her_. He hadn't seen much of this land yet, so he thought he could sail this world for a bit.

Killian sighed staring out in front of him, the sound of the waves calming him.

It was time for him to leave Storybrooke. His heart couldn't take it anymore. After Milah, he didn't think he could love again, but then there was Emma Swan. Fate was playing a cruel joke on him, letting him fall in love with a woman who would never be his. He felt a tear roll down his cheek and he quickly wiped it away. Captain Hook didn't cry, especially not over a woman. But then again, Emma Swan wasn't just any woman. She had slowly crept into his mind and his heart, before he had even realized it.

_-Flashback-_

_They had been in Neverland for four months already and it was beginning to show. The atmosphere on the Jolly Roger had shifted from hopeful to heavy and fearful. The night was falling over Neverland again and still they hadn't come any closer to finding Henry. Killian stood at the helm, steering them to their next adventure, hopefully one where they would find Emma's boy. _

_In the corner of his eye, he saw a figure approaching. He immediately knew who it was._

_"Can't sleep, lass?" he asked, taking in her appearance. She looked as if she hadn't slept in a while, but as always she had her brave face on._

_"Yeah, nothing new," she said and shrugged. It certainly wasn't the first time she paid him a visit while she was supposed to be asleep. _

_He always looked forward to these little moments with her. She finally trusted him and it made him feel all warm inside. Yes, Captain Hook was totally smitten by her. _

_"We will find him, love," he said, knowing her mind was in overdrive again. "I promise." He shifted a bit closer to her as he saw a single tear rolling down her cheek. He wasn't sure how she would react if he'd pull her close to comfort her, but he figured he'd rather try. He tentatively moved closer and wrapped his arms around her, pulling her against him. He was surprised when instead of pushing him away, she leaned into him and let him comfort her. They stood like that for a while, her head cradled into the nook of his neck. His good hand was rubbing circles on her back and she sighed before looking up at him. _

_"Thank you," she said, inching even closer to him. Her gaze flickered to his lips. Killian's breath hitched as he leaned forward a bit. _

_"Emma?" someone behind them said. Killian silently cursed as they moved away from each other and saw Charming coming towards them, glaring at Killian. _

_"Dav- Dad? What are you doing up?" Emma asked embarrassed. _

_"I could ask you the same question," David said._

_"I couldn't sleep," Emma said and shrugged. "So I figured, I go and talk to Hook about the plan for tomorrow." They were going back to the island in the morning. They had been searching for Henry for five months and they finally had located where he was kept. _

_"Talking, huh?" David asked._

_Emma rolled her eyes and walked away, leaving David and Killian alone. _

_"You stay the hell away from my daughter," David said, glaring at Killian. _

_"I think she can decide that for herself," Killian answered and smirked. _

_David took a step closer, fully pissed off. "Don't make me kill you, Hook, because I will." _

_With that David turned around and went to find Emma. _

_-End of flashback-_

His hope had sparked up because of what almost happened. They had gotten pretty close during their journey and he knew the feelings weren't entirely one sided. Killian didn't want to bring it up with them being so close to finding Henry and when they did, he didn't want to be in the way of their reunion. He had broken up a family once and he wasn't about to do it again.

He thought back to the conversation he had with Snow White the day before.

_-Flashback- _

_He heard the bell of the diner, signaling someone had come in, but he didn't bother looking up. _

_"Hey Killian," he heard someone say. He slowly looked up and saw Emma's mother in front of him smiling at him._

_"Your Highness," he said and nodded. _

_"Do you mind if I sat down for a bit?" she said gesturing to the seat next to him. _

_He shrugged and looked down at his plate again. He wasn't hungry, but he figured he had to eat something, since it had been a while. _

_"You okay?" he heard Mary Margaret ask. To say that he was confused would have been an understatement._

_"Why do you care?" he asked quietly. He heard her sigh before reaching for his arm._

_"You saved our lives, Hook. I'm forever indebted to you. And you're not a bad guy so why wouldn't I care?" she answered._

_He met her gaze and was dumbfounded to see she wasn't lying._

_"I also see how you have changed, in the best possible way. I'm really glad you did." she continued._

_Killian frowned and shrugged again. Her daughter was the reason he had changed. He wanted to be a better man because of her, but alas it wasn't meant to be. _

_"David saw you stack your ship today. Are you heading off?" she asked._

_"Yes, you're quite right. There's nothing keeping me here anymore." He said without even bothering to keep the sadness out of his voice._

_"What about Emma?" Snow asked and frowned._

_"What about her?" he asked._

_"She cares about you," she answered. _

_Killian nodded slowly, "But not in the way I want to. I'm sure the lass is grateful like you for getting everyone home safe, but that's all."_

_"I'm sure she-," Snow started as the bell of the diner went again. This time Emma, Henry and Bae walked in. _

_He saw the way they looked at each other. He couldn't and wouldn't stand in the way of that. Bae deserved happiness and Killian was ready to step aside this time. He was ready to swallow down the pain stirring inside of him. He loved Emma, more than he ever thought was possible, but he was willing to rip his own heart out by leaving her. Bae had hurt her, but Emma seemed to have forgiven him. _

_-End of flashback-_

He heard the water slosh against the ship. He looked back at Storybrooke one last time and sighed. His heart was beating furiously in his chest, shooting pains through his body. He would never see Emma again, but his heart was irrevocably hers. He looked back at the ocean and prepared to set sail.

"Killian!" he heard someone shout. His mind was playing tricks on him for sure. "God damn it! Killian!" he heard again. Her voice made his breathing stop and his heart clench. He heard footsteps coming towards him, but he didn't move. He knew that when he looked back, he would see nothing but air. Fate was, yet again, playing a cruel joke on him. He gritted his teeth and looked back anyway, preparing to see nothing.

However, his heart fluttered when he saw someone he didn't expect to see, Emma. He casted his eyes down and sighed, not believing what he had just seen. "You're not real, are you?"

His voice sounded foreign to him, as if it was someone else speaking.

Before he knew it, she had wrapped her arms around him. Silent tears were running down her cheek. "Don't leave," she whispered. "Please, don't leave me."

He frowned and moved his hand to her cheek, wiping away her tears.

He held his breath again, realizing she was really there in his arms. "Emma," he said with a hoarse voice, wrapping his left hand around her waist and pulling her closer.

"I'm sorry, so sorry," she said softly. "I just wanted Henry to have a normal functioning family. I wanted to try for him, even though I didn't want to. I don't love him anymore, Killian. I wish I had chosen you from the start. I wish I had avoided this heartache I've been feeling ever since we came back."

"Shhh, love," he said, holding her tight. "I understand. I just didn't want to break up your family. I didn't want to cause pain to you, Henry, or Bae-Neal."

She looked up at him and he could see her walls crumbling down one by one. Her lips were only inches away from his. Looking into her eyes, he could see she wanted it as much as he did. He closed the gap between them and poured all of his love into this kiss, letting go of his fears. He felt her hands trailing over his back, pulling him even closer to her. He wanted to stay like this forever and never let go. He could feel their kiss going through his whole body. It was as if there were fireworks going on inside.

As they both had to pull up for air, he rested his forehead against her and smiled, his hand cupping her cheek lovingly.

"I love you, Emma Swan," he whispered and brushed his lips over hers. "I love you so much."

Emma smiled up at him, giving him a soft kiss. "I love you too, Killian Jones. I chose you and I will always choose you."

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**This was it. I hope you liked it.**


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